Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cryo-electron microscopy reconstruction of ATP-free ABCA4

ABSTRACT:

SUBMITTER: Jue Chen

PROVIDER: EMPIAR-10808 | biostudies-other |

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

Molecular structures of the eukaryotic retinal importer ABCA4.

Liu Fangyu F Lee James J Chen Jue J

eLife 20210219

The ATP-binding cassette (ABC) transporter family contains thousands of members with diverse functions. Movement of the substrate, powered by ATP hydrolysis, can be outward (export) or inward (import). ABCA4 is a eukaryotic importer transporting retinal to the cytosol to enter the visual cycle. It also removes toxic retinoids from the disc lumen. Mutations in ABCA4 cause impaired vision or blindness. Despite decades of clinical, biochemical, and animal model studies, the molecular mechanism of A ...[more]

PMID: 33605212

Similar Datasets

Cryo-electron microscopy reconstruction of ATP-bound ABCA4 (E1087Q/E2096Q)

Project description: Not available

| EMPIAR-10811 | biostudies-other

Cryo-electron microscopy reconstruction of ATP-bound human P-glycoprotein

Project description: Not available

| EMPIAR-10803 | biostudies-other

Cryo-electron microscopy reconstruction of ATP-bound PCAT1 in an outward-facing conformation in a Mg2+ free condition

Project description: Not available

| EMPIAR-11009 | biostudies-other

Cryo-electron microscopy reconstruction of a poliovirus-receptor-membrane complex.

Project description:To study non-enveloped virus cell entry, a versatile in vitro model system was developed in which liposomes containing nickel-chelating lipids were decorated with His-tagged poliovirus receptors and bound to virus. This system provides an exciting opportunity for structural characterization of the early steps in cell entry in the context of a membrane. Here we report the three-dimensional structure of a poliovirus-receptor-membrane complex solved by cryo-electron microscopy (cryo-EM) at a resolution of 32 A. Methods were developed to establish the symmetry of the complex objectively. This reconstruction demonstrates that receptor binding brings a viral five-fold axis close to the membrane. Density is clearly defined for the icosahedral virus, for receptors (including known glycosylation sites) and for the membrane bilayer. Apparent perturbations of the bilayer close to the viral five-fold axis may function in subsequent steps of cell entry.

| S-EPMC1500892 | biostudies-literature

Random conical tilt reconstruction without particle picking in cryo-electron microscopy.

Project description:A method is proposed to reconstruct the 3D molecular structure from micrographs collected at just one sample tilt angle in the random conical tilt scheme in cryo-electron microscopy. The method uses autocorrelation analysis on the micrographs to estimate features of the molecule which are invariant under certain nuisance parameters such as the positions of molecular projections in the micrographs. This enables the molecular structure to be reconstructed directly from micrographs, completely circumventing the need for particle picking. Reconstructions are demonstrated with simulated data and the effect of the missing-cone region is investigated. These results show promise to reduce the size limit for single-particle reconstruction in cryo-electron microscopy.

| S-EPMC9252301 | biostudies-literature

Cryo-electron microscopy reconstruction of apo bovine MRP1

Project description: Not available

| EMPIAR-10802 | biostudies-other

Practical Experience with Hole-Free Phase Plates for Cryo Electron Microscopy.

Project description:Phase plate (PP) imaging has proven to be valuable in transmission cryo electron microscopy of unstained, native-state biological specimens. Many PP types have been described, however until the recent implementation of the "hole-free" phase plate (HFPP), imaging has been challenging. We found the HFPP to be simple to construct and to set up in the transmission electron microscopy, but care in implementing automated data collection is needed. Performance may be variable, both initially and over time, thus it is important to monitor and evaluate image quality by observing the power spectrum. We found that while some HFPPs gave transfer to high resolution without CTF oscillation, most reached high resolution when operated with modest defocus.

| S-EPMC5241999 | biostudies-literature

Cryo-electron microscopy reconstruction of PCAT1 in three distinct inward-facing conformations during ATP turnover condition

Project description: Not available

| EMPIAR-11010 | biostudies-other

Structure of the mitochondrial ATP synthase from Pichia angusta determined by electron cryo-microscopy.

Project description:The structure of the intact monomeric ATP synthase from the fungus, Pichia angusta, has been solved by electron cryo-microscopy. The structure provides insights into the mechanical coupling of the transmembrane proton motive force across mitochondrial membranes in the synthesis of ATP. This mechanism requires a strong and integral stator, consisting of the catalytic ?3?3-domain, peripheral stalk, and, in the membrane domain, subunit a and associated supernumerary subunits, kept in contact with the rotor turning at speeds up to 350 Hz. The stator's integrity is ensured by robust attachment of both the oligomycin sensitivity conferral protein (OSCP) to the catalytic domain and the membrane domain of subunit b to subunit a. The ATP8 subunit provides an additional brace between the peripheral stalk and subunit a. At the junction between the OSCP and the apparently stiff, elongated ?-helical b-subunit and associated d- and h-subunits, an elbow or joint allows the stator to bend to accommodate lateral movements during the activity of the catalytic domain. The stator may also apply lateral force to help keep the static a-subunit and rotating c10-ring together. The interface between the c10-ring and the a-subunit contains the transmembrane pathway for protons, and their passage across the membrane generates the turning of the rotor. The pathway has two half-channels containing conserved polar residues provided by a bundle of four ?-helices inclined at ?30° to the plane of the membrane, similar to those described in other species. The structure provides more insights into the workings of this amazing machine.

| S-EPMC5111644 | biostudies-literature

2.8 A resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy.

Project description:Recent developments in detector hardware and image-processing software have revolutionized single particle cryo-electron microscopy (cryoEM) and led to a wave of near-atomic resolution (typically ?3.3 Å) reconstructions. Reaching resolutions higher than 3 Å is a prerequisite for structure-based drug design and for cryoEM to become widely interesting to pharmaceutical industries. We report here the structure of the 700 kDa Thermoplasma acidophilum 20S proteasome (T20S), determined at 2.8 Å resolution by single-particle cryoEM. The quality of the reconstruction enables identifying the rotameric conformation adopted by some amino-acid side chains (rotamers) and resolving ordered water molecules, in agreement with the expectations for crystal structures at similar resolutions. The results described in this manuscript demonstrate that single particle cryoEM is capable of competing with X-ray crystallography for determination of protein structures of suitable quality for rational drug design.

| S-EPMC4391500 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data